Hematite nanoparticles commonly undergoes isomorphic substitution of Al3+ in nature, while how the Al-substitution-induced morphological change, defective structure and newly generated Al–OH sites affect the adsorption behavior of hematite for contaminants remains poorly understood. Herein, the interfacial reactions between Al-substituted hematite and Pb2+ was investigated via CD-MUSIC modeling and DFT calculations. As the Al content increased from 0% to 9.4%, Al-substitution promoted the proportion of (001) facets and caused Fe vacancies on hematite, which increased the total active site density of hematite from 5.60 to 17.60 sites/nm2. The surface positive charge of hematite significantly increased from 0.096 to 0.418 C/m2 at pH 5.0 due to the increases in site density and proton affinity (logKH) of hematite under Al-substitution. The adsorption amount of hematite for Pb2+ increased from 3.92 to 9.74 mmol/kg at pH 5.0 and 20 μmol/L initial Pb2+ concentration with increasing Al content. More Fe vacancies may lead to a weaker adsorption energy (Ead) of hematite for Pb2+, while the Ead was enhanced at higher Al content. The adsorption affinity (logKPb) of bidentate Pb complexes slightly increased while that of tridentate Pb complexes decreased with increasing Al content due to the presence of ≡ AlOH−0.5 and ≡ Fe2AlO−0.5 sites. Tridentate Pb complexes were dominant species on the surface of pure hematite, while bidentate ones became more dominant with increasing Al content. The obtained model parameters and molecular scale information are of great importance for better describing and predicting the environmental fate of toxic heavy metals in terrestrial and aquatic environments.